[WIP] Updates (#4)

* begin updates

* rename folders

* let's use literate rather than pluto

* update pairwise alignment

* note outdated tutorial

* remove pluto notebook for RC

* actually note outdated tutorial

Co-authored-by: Kevin Bonham <kevin@bonham.ch>

Author: kescobo

Manifest.toml

@@ -0,0 +1,70 @@
+# This file is machine-generated - editing it directly is not advised
+
+[[Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+
+[[Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+
+[[IOCapture]]
+deps = ["Logging", "Random"]
+git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a"
+uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89"
+version = "0.2.2"
+
+[[InteractiveUtils]]
+deps = ["Markdown"]
+uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+
+[[JSON]]
+deps = ["Dates", "Mmap", "Parsers", "Unicode"]
+git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e"
+uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+version = "0.21.3"
+
+[[Literate]]
+deps = ["Base64", "IOCapture", "JSON", "REPL"]
+git-tree-sha1 = "5b5ec7696d40868945c407f28a6672a230448b70"
+uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+version = "2.13.4"
+
+[[Logging]]
+uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
+
+[[Markdown]]
+deps = ["Base64"]
+uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[[Mmap]]
+uuid = "a63ad114-7e13-5084-954f-fe012c677804"
+
+[[Parsers]]
+deps = ["Dates"]
+git-tree-sha1 = "1285416549ccfcdf0c50d4997a94331e88d68413"
+uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
+version = "2.3.1"
+
+[[Printf]]
+deps = ["Unicode"]
+uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+
+[[REPL]]
+deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
+uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+
+[[Random]]
+deps = ["SHA", "Serialization"]
+uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[[SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+
+[[Serialization]]
+uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
+
+[[Sockets]]
+uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
+
+[[Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"